From dceac420dffa3aa74ef49a50d9be01e450e9d339 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 21 Jul 2020 11:05:00 +0100
Subject: Add sequencer JSON/XML output

---
 test/rest-api.org | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

(limited to 'test')

diff --git a/test/rest-api.org b/test/rest-api.org
index 1930d8b..6dd6616 100644
--- a/test/rest-api.org
+++ b/test/rest-api.org
@@ -53,12 +53,11 @@ When you use the search box on PubSeq it queries the REST end point
 for information on the search items. For example
 
 #+begin_src python :session :exports both
-requests.get(baseURL+"/api/search?s=MT326090.1").json()
+requests.get(baseURL+"/api/search?s=MT533203.1").json()
 #+end_src
 
 #+RESULTS:
-| collection | : | http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126/sequence.fasta | id | : | MT326090.1 | info | : | http://identifiers.org/insdc/MT326090.1#sequence |
-| collection | : | http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126/sequence.fasta | id | : | MT326090.1 | info | : | http://identifiers.org/insdc/MT326090.1#sequence |
+| collection | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta | id | : | MT533203.1 | info | : | http://identifiers.org/insdc/MT533203.1#sequence |
 
 where collection is the raw uploaded data. The hash value in ~c=~ is
 computed on the contents of the Arvados keep [[https://doc.arvados.org/v2.0/user/tutorials/tutorial-keep-mount-gnu-linux.html][collection]] and effectively
@@ -66,10 +65,19 @@ acts as a deduplication uuid.
 
 ** Fetch metadata
 
+Using above collection link you can fetch the metadata in JSON as it
+was uploaded originally from the SHeX expression, e.g. using
+https://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/
+
+But better to use the more advanced sample metadata fetcher
+because is does a bit more in terms of expansion
 
 #+begin_src python :session :exports both
+requests.get(baseURL+"/api/sample/MT533203.1.json").json()
 #+end_src
 
+#+RESULTS:
+
 
 
 ** Fetch EBI XML
-- 
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